Dear Wormers,
Kirk¹s letter promoting his own work represents his opinion and not
scientific facts. Although we have not seen his in press work, his
rationale apparently stems from the viewpoint that parsimony is superior to
other phylogenetic methods, including likelihood.
Since the mid 1990s, likelihood has been repeatedly shown to outperform
other methods of phylogenetic analysis, including parsimony, when examining
sequence data using simulations studies as well as real data sets of yeast
or viruses.
Views similar to what Kirk suggests in his letter have been repeatedly shown
to be problematic also from an abductive viewpoint (for example see, De
Queiroz and Poe 2003 Syst. Biol. 352-367; 2001 Syst. Biol. 305 -321,
Lecointre and Deleporte, 2005 Zoo. Scri. 101-117, Lars Vogt pers. comm.).
Thus, it is clear that the comments were Kirk¹s scientific opinions and not
scientific facts. Last, we assert that the inflammatory tone of Kirk¹s note
does little to promote collegiality or progress in science. Submission as a
peer reviewed comment to Systematic Biology would have been a more
professional venue for critical comments than a list server. At last
contacting the authors before would have be of good matters.
Torsten Struck
Günter Purschke
Ken Halanych
On 3/22/06 2:48 AM, "J. Kirk Fitzhugh" <kfitzhug at nhm.org> wrote:
> Wormers,
>> I was just reading the very interesting paper by Torsten Struck, Gunter
> Purschke, and Ken Halanych in Systematic Biology, 'Phylogeny of Eunicida
> (Annelida) and Exploring Data Congruence Using a Partition Addition Bootstrap
> Alteration (PABA) Approach.' In this paper the authors make the follow
> statement (pp. 54-55):
>> Three general approaches to analyzing multiple data sets (i.e., partitions)
> have been proposed: analyze each partition separately and build a consensus
> tree..., combine partitions prior to analysis..., and combine partitions only
> after certain conditions are met.... For the purposes of our study, we were
> not interested in whether or not to combine data, but were more interested in
> the agreement or disagreement for particular clades across data partitions.
>> I have a paper in a recent issue of Zootaxa (1145), as well as a paper coming
> out this June in Biology & Philosophy that show that the approach taken by
> Struck et al. of conducting partitioned analyses is scientifically
> unacceptable, and the results obtained from such analyses cannot be rationally
> investigated. Any comparisons of phylogenetic hypotheses derived from
> different data sets are entirely meaningless.
>> Struck et al. also rely on so-called 'maximum likelihood' and Bayesian
> approaches to infer hypotheses. As I point out in my Zootaxa paper, the
> notion of likelihood is not correctly applied in 'maximum likelihood' methods
> in phylogenetics, and Bayesian inference is only useful in the process of
> changing beliefs in hypotheses subsequent to confirmation, not as a procedure
> for inferring hypotheses in the first place. I also point out that bootstrap
> methods are applicable to statistical hypotheses, but not to explanatory
> hypotheses.
>> Kirk
>> -----------------------------------------------------
> J. Kirk Fitzhugh, Ph.D.
> Curator of Polychaetes
> Invertebrate Zoology Section
> Research & Collections Branch
> Los Angeles County Museum of Natural History
> 900 Exposition Blvd
> Los Angeles CA 90007
>> Phone: 213-763-3233
> FAX: 213-746-2999
> e-mail: kfitzhug at nhm.org>http://www.nhm.org/research/annelida/staff.html>http://www.nhm.org/research/annelida/index.html> ----------------------------------------------------
>> _______________________________________________
> Annelida mailing list
> Post: Annelida at net.bio.net> Help/archive: http://www.bio.net/biomail/listinfo/annelida> Resources: www.annelida.net
------ NEW CONTACT INFORMATION ------
Dr. Torsten H. Struck
University of Osnabrück
Department of Biology/Chemistry
Zoology
Barbarastrasse 11
D-49069 Osnabrück
Germany
Phone: +49-541-9692859
Fax: +49-541-9692587
e-mail: struck at biologie.uni-osnabrueck.de
